Structure of PDB 3pr5 Chain B

Receptor sequence

>3pr5B (length=341) Species: 2287 (Saccharolobus solfataricus)

MIVLFVDFDYFAAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 3pr5 Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase.
• Chain: B
• Resolution: 2.4 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	B	E106 K152 G185 G187 I189 T190 V296 S297 R298 G299 T301	E106 K152 G185 G187 I189 T190 V296 S297 R298 G299 T301
BS02	dna	B	V32 F37 G41 G218 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 L293 R331 R332 R336	V32 F37 G41 G218 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 L293 R331 R332 R336
BS03	CA	B	A181 I186	A181 I186
BS04	CA	B	D7 F8 D105	D7 F8 D105
BS05	ATP	B	Y10 F11 A12 A44 T45 R51 A57 D105 K159	Y10 F11 A12 A44 T45 R51 A57 D105 K159

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0042276 error-prone translesion synthesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3pr5, PDBe:3pr5, PDBj:3pr5
• PDBsum: 3pr5
• PubMed: 21295588
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)